You have to rest players to get back their energy. Also, the intensity you choose in a match effects the amount of energy you use - with Like There's No Tommorrow (LTNT) using the most, Normal next, and With Next Week In Mind (WNWIM) the least.

So start giving players a rest by not picking them for a game or by only putting them on the bench (but if they come on they will use some energy. If you need to play knackered players tghen you might be better going wnwim, though this will mean you will play badly and if you lose the fans don't like it much. Still, if you are playing a bot team (one that has as its owner 'Private' rather than an actual human manager, in its team home page), then you would probabaly win going WNWIM anyway.

The lower the energy of your players the more chance of injury, so you do need to rest your players sharpish!